Genome-wide identification and analysis of ACP gene family in Brassica species in the Triangle of U model

Abstract Background Acyl carrier proteins (ACP), which have been verified to be involved in a variety of biological processes related to plant growth and development and play a vital role in resisting biotic and abiotic stresses, are widely found in animals, plants, and microbial cells. The Brassica species in the Triangle of U model are not only widely cultivated crops for oilseed and vegetables but also serve as an ideal model for allopolyploid evolutionary analysis. However, the ACP gene family has been largely unknown in Brassica until now. Therefore, comprehensive identification and analysis of this gene family are necessary. Results Based on phylogenetic features and sequence similarity, we identified 26, 27, and 30 ACP genes in the allotetraploid B. juncea (2n = 4x = 36, AABB), B. napus (2n = 4x = 38, AACC), and B. carinata (2n = 4x = 34, BBCC), respectively. Additionally, we identified 14, 10, and 13 ACP genes in the A genome donor B. rapa (2n = 2x = 20, AA), B genome donor B. nigra (2n = 2x = 16, BB), and the C genome donor B. oleracea (2n = 2x = 18, C), respectively. The identified ACP genes (120) in the six Brassica species were classified into six clades. These genes were then chosen for investigation of gene structure and chromosome placement. The findings indicated that the majority of ACP genes maintained consistent gene structures and relatively stable positions on chromosomes. This finding suggests a high level of DNA-level conservation of ACP genes in the six Brassica species following polyploidization. Furthermore, collinearity analysis revealed that the expansion of most Brassica ACPs occurred primarily through segmental duplication during heterotetraploidization, with only a few genes undergoing whole-genome triplication (WGT). Subcellular localization predictions indicated that the ACP gene family of Brassica predominantly localizes to chloroplasts and mitochondria. Additionally, our tobacco transient expression system confirmed that these BnaACPs genes primarily localize to chloroplasts. Furthermore, the analysis of cis -acting regulatory elements revealed the association of these ACP genes with stress tolerance. Additionally, we demonstrated that certain BnaACPs genes exhibited high expression levels in response to salt stress, suggesting their significant role in salt stress response in Brassica species. Conclusion The aforementioned results provide a comprehensive understanding of the ACP genes in Brassica species within the Triangle of U model. Furthermore, our results can serve as a theoretical foundation for further analysis of the functions of ACP genes in Brassica plants.